I'm using DEXSeq to analyze some RNA-seq data. Despite reading the manual
I'm not quite sure I'm doing it correctly for my paired samples. I have for
samples, with the current design for the ExonCountSet:

              condition     experiment
Sample1  treatment         1
Sample2  treatment         2
Sample3  control             1
Sample4  control             2

So the first two samples are the experimental ones, the two last ones
controls, paired with the first two. In the ensuing analysis, I do as
follows:

formula1 = ~ sample + exon + experiment:exon + condition:exon
formula0 = ~ sample + exon + experiment:exon

ecs = estimateDispersions(ecs, minCount=5, nCores=cn, formula=formula1)
ecs = testForDEU(ecs, nCores=cn, formula0=formula0, formula1=formula1)

Is this the correct way to account for the paired nature of my samples?

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